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3D genome sequencing technology in its mid-teens: past, present, and future. 3D基因组测序技术：过去、现在和未来。
IF 16.3 2区 生物学
Trends in Genetics Pub Date : 2025-08-22 DOI: 10.1016/j.tig.2025.07.010
Haoxi Chai, Yijun Ruan
{"title":"3D genome sequencing technology in its mid-teens: past, present, and future.","authors":"Haoxi Chai, Yijun Ruan","doi":"10.1016/j.tig.2025.07.010","DOIUrl":"https://doi.org/10.1016/j.tig.2025.07.010","url":null,"abstract":"<p><p>The genome is packaged with nuclear proteins and RNAs into a complex structure known as chromatin. Its dynamic organization influences genome functions and nuclear properties. Since 2009, high-throughput DNA sequencing methods such as Hi-C and ChIA-PET have pioneered genome-wide mapping of chromatin folding architectures and have given rise to the field of three-dimensional (3D) genome biology. Now, after 15 years of development, this field has experienced a remarkable growth and is still expanding rapidly. It is significantly deepening our understanding of how genome organization affects nuclear functions in various biological systems. In this review we focus on the breakthroughs and expansion of sequencing-based technologies in mapping 3D genomic landscapes and envisage the next frontiers in advancing the 3D genome biology.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":16.3,"publicationDate":"2025-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144978992","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Single-cell omics sequencing technologies: the long-read generation. 单细胞组学测序技术：长读一代。
IF 16.3 2区 生物学
Trends in Genetics Pub Date : 2025-08-22 DOI: 10.1016/j.tig.2025.07.012
Lu Wen, Fuchou Tang
{"title":"Single-cell omics sequencing technologies: the long-read generation.","authors":"Lu Wen, Fuchou Tang","doi":"10.1016/j.tig.2025.07.012","DOIUrl":"https://doi.org/10.1016/j.tig.2025.07.012","url":null,"abstract":"<p><p>Over the past decade, single-cell omics sequencing technologies have revolutionized biological and medical research and deepened our knowledge of cellular heterogeneities in life activities at the genomic, epigenomic, and transcriptomic levels. Concurrently, single-molecule long-read sequencing (SMS) technologies have also made amazingly rapid progress. In recent years, the convergence of these two exciting fields has injected new vitality into the generation of novel insights in genomics (repetitive elements, structural variations), epigenomics (allele-specific epigenetic modifications), and transcriptomics (alternative splicing) at the single-cell level, providing powerful new tools and opening new opportunities for biomedical fields. In this review, we introduce SMS platform-based single-cell genome, epigenome, and transcriptome sequencing technologies - the current situation and future perspectives.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":16.3,"publicationDate":"2025-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144978966","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Formation and biological implications of Z-DNA. Z-DNA的形成及其生物学意义。
IF 16.3 2区 生物学
Trends in Genetics Pub Date : 2025-08-12 DOI: 10.1016/j.tig.2025.07.006
Yonghang Run, Mahmoud Tavakoli, Yuxuan Zhang, Karen M Vasquez, Wenli Zhang
{"title":"Formation and biological implications of Z-DNA.","authors":"Yonghang Run, Mahmoud Tavakoli, Yuxuan Zhang, Karen M Vasquez, Wenli Zhang","doi":"10.1016/j.tig.2025.07.006","DOIUrl":"https://doi.org/10.1016/j.tig.2025.07.006","url":null,"abstract":"<p><p>Z-DNA is a left-handed alternative DNA structure that forms at alternating purine-pyrimidine repeats, which are abundant in genomes. It is intrinsically unstable under physiological conditions; however, it can be stabilized by negative supercoiling and specific Z-DNA binding proteins. These stabilizing factors have prompted renewed interest in the biological significance of Z-DNA within the genome. Emerging evidence suggests that Z-DNA plays critical roles in various cellular processes, including transcriptional regulation, genome instability, chromatin remodeling, and the development of human diseases. This review summarizes existing methodologies for local and global identification of Z-DNA, its genomic and epigenetic features, the factors influencing its formation and stability, its biological implications, and future directions to advance our understanding of Z-DNA biology and its potential applications.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":16.3,"publicationDate":"2025-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144849606","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Unraveling brain complexity: from single-cell to spatial m6A technologies. 解开大脑的复杂性：从单细胞到空间m6A技术。
IF 16.3 2区 生物学
Trends in Genetics Pub Date : 2025-08-12 DOI: 10.1016/j.tig.2025.06.010
Shuangshuang Feng, Magdalena J Koziol
{"title":"Unraveling brain complexity: from single-cell to spatial m<sup>6</sup>A technologies.","authors":"Shuangshuang Feng, Magdalena J Koziol","doi":"10.1016/j.tig.2025.06.010","DOIUrl":"https://doi.org/10.1016/j.tig.2025.06.010","url":null,"abstract":"<p><p>The brain's complexity arises from diverse cell types varying spatially and temporally. N<sup>6</sup>-methyladenosine (m<sup>6</sup>A), the most abundant mRNA modification, regulates gene expression and cellular function. While bulk sequencing studies have provided foundational insights, they obscure m<sup>6</sup>A heterogeneity across cell types and brain regions. Recent advances in single-cell and spatial m<sup>6</sup>A detection technologies have revolutionized our understanding, enabling the exploration of cell-type-specific and spatial m<sup>6</sup>A landscapes. This review discusses the limitations of bulk approaches and highlights emerging single-cell and spatial technologies. We also provide a forward-looking perspective on how technological improvements can further uncover m<sup>6</sup>A's role in brain complexity, offering new opportunities to develop targeted therapies for cell-type-specific m<sup>6</sup>A-marked RNAs.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":16.3,"publicationDate":"2025-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144849607","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The molecular evolutionary basis of species formation revisited. 重新审视物种形成的分子进化基础。
IF 16.3 2区 生物学
Trends in Genetics Pub Date : 2025-08-07 DOI: 10.1016/j.tig.2025.07.003
Megan E Frayer, Nemo V Robles, María José Rodríguez-Barrera, Jenn M Coughlan, Molly Schumer
{"title":"The molecular evolutionary basis of species formation revisited.","authors":"Megan E Frayer, Nemo V Robles, María José Rodríguez-Barrera, Jenn M Coughlan, Molly Schumer","doi":"10.1016/j.tig.2025.07.003","DOIUrl":"https://doi.org/10.1016/j.tig.2025.07.003","url":null,"abstract":"<p><p>How do new species arise? This is among the most fundamental questions in evolutionary biology. The first genetic model for how reproductive barriers lead to the origin of new species was proposed nearly 90 years ago. However, empirical evidence for the genetic mechanisms that cause reproductive barriers took many decades to accumulate. In 2010, Presgraves presented a comprehensive review of the literature on known 'speciation genes' and the possible evolutionary mechanisms through which they arose. Fifteen years later, with an explosion of studies that include both non-model and model organisms, the number of known hybrid incompatibility genes has increased approximately sevenfold. Here, we synthesize previous and new empirical examples to investigate the genetic mechanisms through which intrinsic incompatibilities in hybrids arise and highlight current gaps in our understanding.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":16.3,"publicationDate":"2025-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144805321","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Selfish B chromosome evades genome elimination. 自私的B染色体逃避了基因组的消除。
IF 16.3 2区 生物学
Trends in Genetics Pub Date : 2025-08-01 Epub Date: 2025-06-16 DOI: 10.1016/j.tig.2025.05.008
Cécile Courret
{"title":"Selfish B chromosome evades genome elimination.","authors":"Cécile Courret","doi":"10.1016/j.tig.2025.05.008","DOIUrl":"10.1016/j.tig.2025.05.008","url":null,"abstract":"<p><p>The mealybug B chromosome evades paternal genome elimination (PGE) by mimicking maternal chromatin states, ensuring its transmission. Vea et al. conducted a detailed genomic and transcriptomic analysis, highlighting a histone acetyltransferase potentially driving this behavior. Their findings illuminate selfish chromosome strategies and epigenetic manipulation of inheritance systems.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"637-639"},"PeriodicalIF":16.3,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144318725","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Molecular circuits for genomic recording of cellular events. 细胞事件基因组记录的分子电路。
IF 16.3 2区 生物学
Trends in Genetics Pub Date : 2025-08-01 Epub Date: 2025-05-06 DOI: 10.1016/j.tig.2025.04.004
Wei Chen, Junhong Choi
{"title":"Molecular circuits for genomic recording of cellular events.","authors":"Wei Chen, Junhong Choi","doi":"10.1016/j.tig.2025.04.004","DOIUrl":"10.1016/j.tig.2025.04.004","url":null,"abstract":"<p><p>Advances in precise genome editing are enabling genomic recordings of cellular events. Since the initial demonstration of CRISPR-based genome editing, the field of genomic recording has witnessed key strides in lineage recording, where clonal lineage relationships among cells are indirectly recorded as synthetic mutations. However, methods for directly recording and reconstructing past cellular events are still limited, and their potential for revealing new insights into cell fate decisions has yet to be realized. The field needs new sensing modules and genetic circuit architectures that faithfully encode past cellular states into genomic DNA recordings to achieve such goals. Here we review recently developed strategies to construct diverse sensors and explore how emerging synthetic biology tools may help to build molecular circuits for genomic recording of diverse cellular events.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"647-659"},"PeriodicalIF":16.3,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12324969/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144044657","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
New dimensions in the molecular genetics of insect chemoreception. 昆虫化学接受分子遗传学的新维度。
IF 16.3 2区 生物学
Trends in Genetics Pub Date : 2025-08-01 Epub Date: 2025-05-07 DOI: 10.1016/j.tig.2025.04.003
Gaëlle J S Talross, John R Carlson
{"title":"New dimensions in the molecular genetics of insect chemoreception.","authors":"Gaëlle J S Talross, John R Carlson","doi":"10.1016/j.tig.2025.04.003","DOIUrl":"10.1016/j.tig.2025.04.003","url":null,"abstract":"<p><p>Chemoreception is the foundation of olfaction and taste, which in insects underlie the detection of humans to whom they spread disease and crops that they ravage. Recent advances have provided clear and in some cases surprising new insights into the molecular genetics of chemoreception. We describe mechanisms that govern the choice of a single Odorant receptor gene by an olfactory receptor neuron in Drosophila. We highlight genetic and epigenetic mechanisms by which chemoreceptor expression can be modulated. Exitrons, RNA editing, and pseudo-pseudogenes in chemosensory systems are described. We summarize key insights from the recent structural determinations of odorant and taste receptors. Finally, new molecular components of chemosensory systems, including long noncoding RNAs, are described.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"706-715"},"PeriodicalIF":16.3,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12324945/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144063273","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Polyploidy in potatoes: challenges and possibilities for climate resilience. 马铃薯多倍体：气候适应能力的挑战和可能性。
IF 16.3 2区 生物学
Trends in Genetics Pub Date : 2025-08-01 Epub Date: 2025-04-22 DOI: 10.1016/j.tig.2025.03.006
Helen H Tai, Laura M Shannon, Martina V Strömvik
{"title":"Polyploidy in potatoes: challenges and possibilities for climate resilience.","authors":"Helen H Tai, Laura M Shannon, Martina V Strömvik","doi":"10.1016/j.tig.2025.03.006","DOIUrl":"10.1016/j.tig.2025.03.006","url":null,"abstract":"<p><p>Solanum section Petota Dumort. consists of tuber-bearing species (i.e., the cultivated potatoes and their wild relatives) that have both asexual and sexual propagation, variation in ploidy, and reproductive isolation. These species have undergone adaptation to a diversity of climates, altitudes, photoperiods, and geographical range. The section defies characterization with the biological species concept due to interspecies hybridization, allo- and auto-polyploidy, and phenotypic plasticity. Genetic studies, and more recently genome sequencing and pangenome analyses, are fostering a greater understanding of genetic processes that shape genome evolution and speciation in the section, shedding light on the phylogeny and providing insights on utilization of potato crop wild relatives in breeding for climate-resilient potato varieties.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"716-723"},"PeriodicalIF":16.3,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144018844","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Strategies for studying sex differences in brain aging. 研究脑老化性别差异的策略。
IF 16.3 2区 生物学
Trends in Genetics Pub Date : 2025-08-01 Epub Date: 2025-03-04 DOI: 10.1016/j.tig.2025.02.001
Victor A Ansere, Seung-Soo Kim, Francesca Marino, Katherine Morillo, Dena B Dubal, Coleen T Murphy, Yousin Suh, Bérénice A Benayoun
{"title":"Strategies for studying sex differences in brain aging.","authors":"Victor A Ansere, Seung-Soo Kim, Francesca Marino, Katherine Morillo, Dena B Dubal, Coleen T Murphy, Yousin Suh, Bérénice A Benayoun","doi":"10.1016/j.tig.2025.02.001","DOIUrl":"10.1016/j.tig.2025.02.001","url":null,"abstract":"<p><p>Studying sex effects and their underlying mechanisms is of major relevance to understanding brain health. Despite growing interests, experimentally studying sex differences, particularly in the context of aging, remains challenging. Since sex chromosomal content influences gonadal development, separating the effects of gonadal hormones and chromosomal factors requires specific model systems. Here, we highlight rodent and tractable models for examining sex dimorphism in brain and cognitive aging. In addition, we discuss multi-omic and bioinformatic approaches that yield biological insights from animal and human studies. This review provides a comprehensive overview of the diverse toolkit now available to advance our understanding of sex differences in brain aging.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"678-690"},"PeriodicalIF":16.3,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12324943/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143558825","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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